[med-svn] [Git][med-team/cyvcf2][master] Commit NMU from Stefano Rivera

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / cyvcf2


Commits:
df9ade50 by Andreas Tille at 2021-11-21T14:23:50+01:00
Commit NMU from Stefano Rivera

- - - - -


3 changed files:

- debian/changelog
- + debian/patches/python-3.10.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+cyvcf2 (0.30.11-1.1) unstable; urgency=medium
+
+  * Non-maintainer upload.
+  * Patch: Python 3.10 support - avoid a regression in gzip file handles
+    (Closes: #1000317)
+
+ -- Stefano Rivera <stefanor at debian.org>  Sun, 21 Nov 2021 08:38:57 -0400
+
 cyvcf2 (0.30.11-1) unstable; urgency=medium
 
   * Fix watch URL


=====================================
debian/patches/python-3.10.patch
=====================================
@@ -0,0 +1,46 @@
+From: Stefano Rivera <stefano at rivera.za.net>
+Date: Sun, 21 Nov 2021 08:29:40 -0400
+Subject: Avoid a Python 3.10 regression in iterating GzipFiles
+
+Open the file with a context manager, so we're holding onto a reference to it, for the lifetime of the iteration.
+
+This avoids hitting https://bugs.python.org/issue45475 which affects python3.10 3.10.0-4 in Debian.
+
+Bug-Debian: https://bugs.debian.org/1000317
+Forwarded: https://github.com/brentp/cyvcf2/pull/225
+---
+ cyvcf2/tests/test_reader.py | 21 +++++++++++----------
+ 1 file changed, 11 insertions(+), 10 deletions(-)
+
+diff --git a/cyvcf2/tests/test_reader.py b/cyvcf2/tests/test_reader.py
+index 76cb9f8..f81b920 100644
+--- a/cyvcf2/tests/test_reader.py
++++ b/cyvcf2/tests/test_reader.py
+@@ -456,16 +456,17 @@ def test_var_type():
+ def _get_line_for(v):
+     import gzip
+ 
+-    for i, line in enumerate(gzip.open(VCF_PATH), start=1):
+-        line = line.decode()
+-        if line[0] == "#": continue
+-        toks = line.strip().split("\t")
+-        if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue
+-        if toks[3] != v.REF: continue
+-        if toks[4] not in v.ALT: continue
+-        return toks
+-    else:
+-        raise Exception("not found")
++    with gzip.open(VCF_PATH) as f:
++        for i, line in enumerate(f, start=1):
++            line = line.decode()
++            if line[0] == "#": continue
++            toks = line.strip().split("\t")
++            if not (toks[0] == v.CHROM and int(toks[1]) == v.POS): continue
++            if toks[3] != v.REF: continue
++            if toks[4] not in v.ALT: continue
++            return toks
++        else:
++            raise Exception("not found")
+ 
+ 
+ def _get_samples(v):


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 add_htslib_link_dependency.patch
 i386.patch
+python-3.10.patch



View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734

-- 
View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/commit/df9ade504e530e167fdaf16ea4ced6a6a4eb9734
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20211121/8cc55c7b/attachment-0001.htm>